Question

I have the following code that uses ‘paste’ and AWK script inside Perl.

use strict;               use Data::Dumper;         use Carp; use File::Basename;        my @files = glob('result/*-*.txt'); my $tocheck = $ARGV[0] || 'M';   foreach my $file ( @files  ) {     my $base = basename($file,'.txt');     my @res = `paste <\(awk '\$4 == 'M' {sum += \$2 }END{print sum}' $file \) <\(awk '\$4 == 'M' {sum += \$3 }END{print sum}' $file\)`;     chomp(@res);              print '$base $res[0]\n';      }  

Why it gives such error:

#sh: -c: line 1: syntax error near unexpected token `(' #sh: -c: line 1: `paste <(awk '$4 == 'M' {sum += $2 }END{print sum}' result/9547_1-S_aureus.txt ) <(awk '$4 == 'M' {sum += $3 }END{print sum}'  #result/9547_1-S_aureus.txt) 

What’s the correct way to do it?

Answer 1

Not entirely sure if this is a correct interpretation of your script, as there appears to be a lot of dead/unused code there, but there is certainly no need to go spawning paste or awk to do this:

#!/usr/bin/perl use warnings; use strict; use File::Basename;  my @files = glob ('result/*-*.txt');  foreach my $file (@files) {    open (FILE, $file) or die 'open $file: $!\n';    # You seem to be summing the 2nd and 3rd columns if the 4th is 'M'    my ($col1, $col2) = (0, 0);    while (<FILE>) {        my @cols = split /\s+/;        if ($cols[3] eq 'M') {           # Perl uses 0-based arrays, unlike awk           $col1 += $cols[1];           $col2 += $cols[2];        }    }    close FILE;    printf '%s %d\n', basename ($file), $col1; }